Reports say the Aurukun primary school massively overstated its student numbers by accident.

A review of the school run in partnership with Indigenous leader Noel Pearson’s Good to Great Schools organisation has found it routinely overstated enrolments and netted up to $815,000 in extra payments.

Acting auditor-general Anthony Close said student numbers were not deliberately inflated, but came as a result of poor record keeping and misinterpreted policy.

There was no deliberate mismanagement and “no evidence of financial impropriety” in the schools public funding, he said.

Mr Close said poor financial stewardship by the Education Department was partly to blame.

Good to Great Schools Australia (GGSA) leader Noel Pearson said the review process had damaged the Cape York Academy's reputation.

Mr Pearson said the report gave “important confirmation that GGSA played no role or had responsibility in these matters”.

“[The auditor-general] has given a clean bill of health to the financial and administrative practices of Good to Great Schools Australia's role with the [academy],” he said in a statement.

“GGSA places on record our dismay and concern at the curious release of sections of those previous reports to media, which damaged GGSA's reputation and jeopardised our students' education.

“Those within the department responsible for the leaking should be exposed and held to account.”

Queensland’s education director-general ordered the review after an internal audit last year found a number of high-risk business practices, which led to thousands of dollars in payments and purchases not being adequately explained.

The latest review found student enrolment numbers were over-reported by 116 between 2010 and 2016, resulting in the Government providing $815,000 in base funding to the school that it may not have been entitled to.

The auditors found no evidence of deliberate manipulation.

Mr Close said the numbers were fudged because school staff incorrectly interpreted Education Department policy and guidelines.

“Aurukun school staff who processed student enrolments did not confirm the identity, custody, and age of children,” he said.

Additionally, a Memorandum of Understanding (MoU) between the Government and GGSA was partly to blame.

“The MoU did not contain essential elements to allow DET to successfully manage a long-term partnership,” Mr Close wrote.

The auditor’s report made three recommendations: stronger agreements between private operators and the state, better training for staff, and more reviews to make sure the recommendations are implemented.